GEN-MKT-18-7897-A
May 24, 2016 | Blogs | 0 comments
In part 1 and part 2 of this blog series we discussed how you can increase your efficiency for high throughput quantitative proteomics by industrializing your sample analysis and data processing. Microflow SWATH® Acquisition on your TripleTOF® system coupled with OneOmics™ data analysis tools allow you to run samples faster, collect data faster, and process your data files faster. It all adds up to getting more meaningful biological information in a shorter amount of time.
Except there’s still one problem. Your sample preparation is now the bottleneck. Your time is too valuable to waste on repetitive pipetting. It’s time to revolutionize your sample preparation and industrialize your entire workflow! Whether you’re working with biological fluids, cell lines, or tissues, there are automated strategies that can alleviate the time-sink of manual sample preparation.
Researchers from SCIEX, Cedars Sinai Medical Center, and Beckman Coulter demonstrate the advantages of using a Biomek NXP Span-8 Workstation and Protein Preparation Kits with ready-to-use reagents and methods to automate protein digestion of biofluids. The Biomek workstation puts every aspect of liquid handling – including pipetting, dilution, dispensing and integration – into a single, automated system. The all-in-one protein preparation kits provide all the reagents for automated protein denaturation, reduction, alkylation, and trypsin digestion for 96 samples at a time. Besides automating routine tasks and freeing valuable researcher time, they also reduce day-to-day variability resulting from a manual, time-consuming, multi-step protocol.
As demonstrated, very high day-to-day reproducibility within a lab, as well as between different labs, can be obtained. Over 80% of peptides monitored by LC-MS had digestion reproducibility below 10% CVs. And most importantly, similar performance was observed in multiple labs on multiple days1.
The end result – higher reproducibility, higher efficiency, less personal burden for mundane tasks, and more valuable time for other research inquiries.
Learn more about how Dr. Jenny van Eyk and her team are developing robust pipelines for targeted proteomic analysis to do population-scale proteomics by watching her webinar2: Proteome Centric Precision Medicine – Embracing Pathological Diversity.
The Biomek workstation and protein preparation kits are an excellent solution for liquid phase samples, biological fluids, and cell lines. But what if you’re working with tissues or tumors or other complex or challenging biospecimens?
Here’s where the PCT-HD Pressure Cycling Technology High Definition sample preparation system can help. PCT-HD sample preparation enables faster, less cumbersome and higher quality homogenization, extraction and digestion of proteins from tissue samples by utilizing controlled cycles of pressure to break apart the samples. This process results in faster and improved sample processing, and a higher quality of results.
As demonstrated in a recent webinar3, the PCT-HD provides hands-free sample homogenization and integrated disposable tools for up to 16 samples per batch. PCT also helps to digest not only poorly soluble membrane proteins, but also many tightly folded proteins that can resist digestion under conventional conditions. The method takes less than 40 minutes of hands-on operator time and is completed in about 4 hours, including a post-digestion sample clean-up with solid phase extraction columns.
The end result – faster sample preparation for tissue samples that provides even better results than manual preparation.
Learn more about how PCT sample preparation combined with SWATH acquisition can provide high-quality quantitative data for tissue proteomics in this webinar4 by Dr. Tiannan Guo from Professor Ruedi Aebersold group (Institute of Molecular Systems Biology, ETH Zurich).
Finally, maintaining an industrialized quantitation proteomics pipeline also requires quality control and performance benchmarking. SCIEX will soon launch a SWATH Acquisition Performance Kit which provides samples and methods for assessing the status of your LC-MS system, for getting started on running SWATH experiments and for benchmarking the data quality of your SWATH results.
So don’t let sample prep be your rate-limiting step! To learn more about how you can revolutionize and industrialize your sample preparation protocol, read the full technical note1 and view the webinars2,3,4. And to see how you can industrialize your entire proteomics workflow to improve your efficiency and save valuable time during sample analysis and data analysis, see part 1 and part 2 of this blog series.
References
Trifluoroacetic acid (TFA) is emerging as one of the most concerning ultrashort-chain PFAS in Europe’s food supply – particularly in cereals, a staple consumed daily by millions. A report from PAN Europe reveals a widespread and largely unmonitored contamination trend that raises serious questions about food safety, regulatory blind spots, and future monitoring strategies.
PFAS analysis is complex, but expert guidance doesn’t have to be. In this episode of our ‘Ask the PFAS expert series’, we’re joined by Michael Scherer, Application Lead for Food and Environmental, to answer the most pressing questions in PFAS analysis. From why LC-MS/MS systems are the gold standard for analyzing diverse PFAS compounds, to which EU methods deliver reliable results for drinking water, and to practical steps to prevent contamination, Michael shares actionable insights to help laboratories achieve accuracy, consistency, and confidence in their workflows.
During an LC-MS/MS experiment, traditional fragmentation techniques like collision-induced dissociation (CID) have long been the gold standard. Electron-activated dissociation (EAD) is emerging as a transformative tool that enhances structural elucidation, particularly for complex or labile metabolites.
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